Normal Modes.
To compute low-frequency modes using the Elastic Network Model in an all-atom
representation (if you wish), try:
ELNEMO (K.Suhre);
to be upgraded to:
ELNEMO2 (under development);
there, you can also generate a set of "perturbed" structures,
so as to mimic the functional flexibility of your system (e.g. a protein),
by distorting it along one or two of its low-frequency modes.
This can prove useful for solving difficult molecular replacement problems,
for instance. A related dowloadable tool, called
NORMA,
allows for flexible fitting of high-resolution protein structures into
low-resolution electron-microscopy density maps.
ELNEMO and NORMA use the fortran 77 programs
PDBMAT and DIAGRTB,
which are freely available.
PDBMAT computes the Hessian, using the Elastic Network Model.
DIAGRTB yields the low-frequency normal modes, by diagonalizing the Hessian,
using the RTB approximation.
For not too large systems,
BLZPACK (BLock lancZos PACKage) is a very efficient diagonalizer.
It is available from
the homepage of Osni Marques.
Nonlinear models can also be considered, using nnmdw.
AD-ENM (B.R.Brooks)
and
ANM (I.Bahar)
use the same Elastic Network Model as ELNEMO,
but allows only for a single-atom per residue
representation.
ENCoM (Najmanovich) and
WEBnm@ (K.Hinsen)
use other kinds of Elastic Network Models, also with a single-atom per residue
representation. The later model has been used to generate a database of motion movies:
NMA-Movie (M.Gerstein).
For computing atom fluctuations (B-factors), using an even simpler protein model (sic):
GNM (I.Bahar).
ProMode (N.Go):
is a database of modes computed with FEDER (all-atoms, dihedral coordinates,
empirical potential; for proteins with less than 300 aa).
For small proteins (less than 150 aa), you can compute them at the same level of detail,
using GROMACS, with:
NOMAD-ref (M.Delarue).
In this later site a lot of tools are available, for performing normal
mode analyses, structure refinment, etc.
To learn about the underlying methods, there is a rather recent
Book,
edited by Ivet Bahar and Qiang Cui.
To get a flavor of what the modes of a simple object may look like,
the low-frequency vibrations of a free sphere can be viewed in
3D,
as well as those of the
Earth.